From 4b2ba92ebd48e201420c0fbe3894101d2df85b39 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Wed, 11 Mar 2026 14:19:43 -0500 Subject: [PATCH 1/2] Add 6.1 releases page to toctree --- docs/releases.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/releases.rst b/docs/releases.rst index 981cd8856..2dd703dce 100644 --- a/docs/releases.rst +++ b/docs/releases.rst @@ -28,3 +28,4 @@ Release Notes releases/5_4 releases/5_5 releases/6_0 + releases/6_1 From cb56e599f3d88a1c0674c842362455544c78fca4 Mon Sep 17 00:00:00 2001 From: Maksim Filippov Date: Tue, 17 Mar 2026 23:56:50 +0000 Subject: [PATCH 2/2] Remove pdb debugger left in production output_parser code Replaces bare except/pdb.set_trace() with a proper KeyError that includes context about the missing wildtype position and epitope sequence. --- pvactools/lib/output_parser.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/pvactools/lib/output_parser.py b/pvactools/lib/output_parser.py index 56fc86d80..14f77dd17 100644 --- a/pvactools/lib/output_parser.py +++ b/pvactools/lib/output_parser.py @@ -210,9 +210,8 @@ def match_wildtype_and_mutant_entry_for_missense(self, result, mt_position, wt_r mt_epitope_seq = result['mt_epitope_seq'] try: wt_result = wt_results[match_position] - except: - import pdb - pdb.set_trace() + except KeyError: + raise KeyError(f"No wildtype result found at position {match_position} for MT epitope {mt_epitope_seq}") wt_epitope_seq = wt_result['wt_epitope_seq'] result['wt_epitope_position'] = match_position total_matches = self.determine_total_matches(mt_epitope_seq, wt_epitope_seq)